Few, if any, protozoan parasites are reported to parasitize two very different host species and exhibit extreme organ tropism like the flagellate Tritrichomonas foetus. In cattle, this parasite causes extensive damage to the uterine lining which results in abortion while infection in domestic cats causes chronic diarrhoea. Whilst single-gene comparisons and cross-infectivity studies suggest that these two strains fall under the same T. foetus species-level umbrella, little is known of their strain-specific characteristics. Analysis of the transcribed RNA offers an ideal means of investigating regulatory patterns and preferentially expressed genes. In the absence of a T. foetus genome, we employed a de novo approach to characterize the whole-cell transcriptome of a bovine and feline strain with the aim of providing a more dynamic approach of understanding cell-wide processes and virulence factors in T. foetus. This provides the first comprehensive cell-wide transcriptomics analysis of the bovine and feline T. foetus strains and aims to identify to what extent the expressed T. foetus genomereflects the host from which it was isolated.